Difference between stacking and extruding meshes?
I would recommend using one mesh. You can easily get the mesh you want in this instance by selecting the desired face, pressing E to extrude and then S to scale. Now press E to extrude again, and you have the desired mesh, created in three simple commands.



This method works in many other instances, even on N-Gon or Tri faces. This is a good general modelling technique to know for any modelling project.